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This is the command bp_taxonomy2treep that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


bp_taxonomy2tree - Building a taxonomic tree based on the full lineages of a set of
species names

DESCRIPTION


This scripts looks up the provided species names in the NCBI Taxonomy database, retrieves
their full lineage and puts them in a Newick taxonomic tree displayed on screen.

bp_taxonomy2tree.pl -s Orangutan -s Gorilla -s Chimpanzee -s Human
bp_taxonomy2tree.pl -s Orangutan -s Gorilla -s Chimpanzee -s "Homo Sapiens"

Can also provide -d to specify the directory to store index files in, -o to specify the
location of your NCBI nodes file, and -a for the NCBI names file. Or the option -e to use
the web-based Entrez taxonomy database if you do not have the NCBI flatfiles installed.

This script requires that the bioperl-run pkg be also installed.

Providing the nodes.dmp and names.dmp files from the NCBI Taxonomy dump (see
Bio::DB::Taxonomy::flatfile for more info) is only necessary on the first time running.
This will create the local indexes and may take quite a long time. However once created,
these indexes will allow fast access for species to taxon id OR taxon id to species name
lookups.

AUTHOR - Gabriel Valiente, reimplemented by Sendu Bala


Email [email protected] Email [email protected]

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